Abstract
Caesalpinia sappan Linnaeus is a great tree of Fabaceae. It is mainly distributed in the Southern provinces of China and Southeast Asian countries. It can be used to extract dyes. The heartwood has dyestuff and medicinal value. There is no study on the genome of C. sappan so far. Here, we report and characterize the complete plastid genome sequence of C. sappan in an order to provide genomic resources useful for promoting its conservation. The complete chloroplast genome of C. sappan is 160,176 bp in length with a typical quadripartite structure, consisting of a large single-copy region (LSC, 89,710 bp), a single-copy region (SSC, 18,357 bp), and a pair of inverted repeats (IRs, 26,054 bp). There are 129 genes annotated, including 84 unique protein-coding genes, eight unique ribosomal RNA genes, and 37 transfer RNA genes. The overall G/C content in the plastome of C. sappan is 36.0%. The complete plastome sequence of C. sappan will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Apocynaceae.
Caesalpinia sappan Linnaeus is a plant of the family Fabaceae, mainly distributed in Southern provinces of China, for example, Guangdong, Guangxi, Yunnan, Guizhou, Hainan, and Southeast Asian countries. It is a plant that combines dyestuff and medicinal value (Chen et al. Citation1965). The chloroplast genome sequence carries rich information for plant molecular systematics and Barcoding. To date, there have been no studies on the genome of C. sappan. To provide a rich genetic information and improve C. sappan molecular breeding in the future, we report and characterize the complete plastid genome sequence of C. sappan (GenBank accession number: MT505712).
In this study, the fresh leaves of C. sappan were collected from Jianfeng Mountain Hainan province (108.88° E, 18.73° N). Voucher specimens (HUTB 187224) were deposited in the Herbarium of the Institute of Tropical Agriculture and Forestry (code of herbarium: HUTB), Hainan University, Haikou, China.
The experiment procedure was as reported in Wang et al. (Citation2019). The total DNA of the C. sappan was sequenced with second-generation sequencing technology (Illumina HiSeq 2000, San Diego, CA). The chloroplast genome sequence reads were assembled with bioinformatic pipeline including SOAP2 software (Li et al. Citation2009) and several runs of manual corrections of sequence reads. Genes encoded by this genome were annotated by import the fasta format sequence to the DOGMA (Wyman et al. Citation2004) and recorrected by manual. The results showed that plastome of C. sappan possesses a total length of 160,176 bp with the typical quadripartite structure of angiosperms, containing two Inverted Repeats (IRs) of 26,054 bp, a Large Single-Copy(LSC) region of 89,710 bp, and a Small Single-Copy (SSC) region of 18,357 bp. The plastome contains 129 genes, consisting of 88 unique protein-coding genes, 37 unique tRNA genes, and eight unique rRNA genes. The overall G/C content in the plastome of C. sappan is 36.0%, in which the corresponding values of the LSC, SSC, and IR region were 33.40%, 29.90%, and 42.60%, respectively.
We used RAxML (Stamatakis Citation2006) with 1000 bootstraps under the GTRGAMMAI substitution model to reconstruct a maximum-likelihood (ML) phylogeny of 13 published complete plastomes of Fabaceae and Surianaceae, using Suriana maritima (Surianaceae) as outgroups. According to the phylogenetic topologies, C. sappan was closely related to Mezoneuron cucullatum. Most nodes in the plastome ML trees were strongly supported (). The complete plastome sequence of C. sappan will provide a useful resource for the conservation genetics of this species as well as for the phylogenetic studies for Fabaceae.
Figure 1. Maximum-likelihood phylogenetic tree based on 13 complete chloroplast genomes. Accession number: Caesalpinia sappan (this study); Barklya syringifolia NC_037761.1; Barnebydendron riedelii NC_047396.1; Butea monosperma NC_047384.1; Cercis chunianaMF741770.1; Daniellia pilosa NC_036744.1; Erythrophleum fordii NC_041164.1; Goniorrhachis marginataNC_047394.1; Maackia floribunda NC_034774.1; Mezoneuron cucullatumNC_047386.1; Parkinsonia africanaNC_047387.1; outgroup: Suriana maritima MK830069.1. The number on each node indicates the bootstrap value.
Disclosure statement
The authors report that they have no conflicts of interest. The authors alone are responsible for the content and writing of the paper.
Data availability statement
The data that support the findings of this study are openly available in GenBank of NCBI at http://www.ncbi.nlm.nih.gov, reference number MT505712.
Additional information
Funding
References
- Chen HY. 1965. Flora of Hainan. Vol. 2. Beijing (People’s Republic of China): Science Press. p. 227.
- Li RQ, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. 2009. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 25(15):1966–1967.
- Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):2688–2690.
- Wang HX, Chen L, Cheng XL, Chen WS, Li LM. 2019. Complete plastome sequence of Callicarpa nudiflora Vahl (Verbenaceae): a medicinal plant. Mitochondrial DNA B. 4(2):2090–2091.
- Wyman SK, Jansen RK, Boore JL. 2004. Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 20(17):3252–3255.